Abstract
The stomach bacterium Helicobacter pylori has a long and intimate association with humans, possibly since the dawn of humanity. It causes a variety of upper gastrointestinal disorders, including chronic gastritis, peptic ulcer disease and gastric cancer. It is ubiquitously present and infects almost 50% of humans worldwide. Its high prevalence and mode of transmission within families or close bio-geographic populations, along with its high genetic variability make it a useful marker for tracing human migration. New generation sequencing technology has been successfully applied to retrieve ancient H. pylori DNA from intestinal soft tissues and gut content of a few mummies across the world, including the Tyrolean glacial mummy known as "Ötzi", whose 5,300-year-old H. pylori genome represents the only so far reconstructed ancient H. pylori genome.
In this study, we reconstructed the genome of an ancient H. pylori strain from the mummified human remains of Anna Catharina Bischoff, an upper-class member of post-reformed Basel. By using an enrichment capture approach designed to target H. pylori DNA, we obtained an average 47x coverage across the 18th century genome. Further investigations aim to create a de novo assembly of the genome to increase its completeness as well as study possible recombination events and genomic rearrangement which is not discernible with alignment based methods alone. By comparing the ancient H. pylori genome with the vast amount of available modern European H. pylori genomes, we aim to shed new light on the diversity of H. pylori in 18th century Europe.